Chronic obstructive pulmonary disease (COPD) is a chronic debilitating disease that afflicts ~24 million Americans and is a major cause of death and disability globally. Research over the past 2 decades has begun to elucidate the critical role of bacterial colonization and infection, particularly by nontypeable Haemophilus influenzae (NTHI), in the course and pathogenesis of COPD. In an 18-year ongoing prospective study, we have established that a large proportion of adults with COPD show persistent airway colonization by NTHI. Although such colonization was previously thought to be innocuous because of the absence of acute symptoms, it is now clear that such colonization contributes to the airway inflammation and impaired pulmonary function that are hallmarks of COPD. The carefully characterized strains from this long-term study allow us to address key areas where opportunities to develop novel interventions in the course of COPD exist. In aim 1 the evolutionary dynamics of the NTHI genome from serial isolates that lived in the complex environment of the human airways will be elucidated to identify adaptations that facilitate persistence in the airways in COPD. In aim 2 the effect of immune selective pressure on candidate vaccine antigens will be elucidated. Vaccine development for NTHI is undergoing exciting new developments with the recent licensing of a vaccine that contains an NTHI antigen and preclinical and clinical development of several additional antigens. Monitoring the effect of persistence in the human respiratory tract in driving sequence changes and their consequences on candidate vaccine antigens is critical to assessing such vaccine candidates. In aim 3 the frequency of antimicrobial resistance markers and tolerance in NTHI that colonize and infect adults with COPD will be studied to assess the effect of antibiotic use in driving resistance mechanisms. The genomes of bacteria harbor antibiotic resistance markers that are undetected by simply measuring antimicrobial susceptibility and thus allow us to anticipate future antibiotic resistance mechanisms. Antibiotic tolerance, a term that refers to persistence in the face of active antibiotic, will be explored as a mechanism of persistence in COPD. It is now clear that chronic bacterial colonization of the airways is a major contributor to airway inflammation and impaired pulmonary function in COPD. The application of state-of-the-art methods to a unique set of strains and detailed associated data make it possible to explore 3 key areas that are unexplored: 1) mechanisms of persistence, 2) the effect of persistence on vaccine antigens and 3) the role of repeated antibiotic exposure in driving antibiotic resistance and tolerance as mechanisms of persistence. Each of these 3 areas is rich in opportunities to develop novel interventions in the course of COPD.